E-RNAi can receive sequences from the generic genome browser GBrowse using the GBrowse input option.
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Selection of the organism
The entry page allows the selection of the desired organism (C. elegans in the example above). Using the 'GBrowse' button the session is started.
This page describes how to submit sequences from GBrowse to E-RNAi. The communication works via a 'design ID' that is unique to a session started. By following the instructions on this page, target sequences can be easily searched and selected from GBrowse.
GBrowse opens in a new tab from the link indicated. In GBrowse genes can be searched by available identifiers or by absolute genomic positions (in the format chromosome:start..end) through the 'Landmark or Region' box. In the example below F48E3.4, an isoform of the C. elegans gene WBGene00018606, was queried.
In the visualization of the queried gene model, regions can be selected by keeping the left mouse button pressed and sliding over the desired region. Once the left mouse button is released, a menu opens containing the option 'Submit selection to E-RNAi'.
On the page that opens up the selected sequence is shown together with a text box where the design ID needs to be pasted to proceed.
'Confirm' will submit the sequence to E-RNAi and a validation page with an overview about all sequences submitted for this design ID will appear.
Both, the confirmation and evaluation pages can be closed and GBrowse can be used to submit another sequence (for up to 50 sequences). Finally, also the GBrowse page can be closed. By clicking the 'Update Selection' button on the entry page a final overview about the submitted sequences will be provided, also allowing to decide whether long dsRNAs or siRNAs should be designed.
The 'Submit Selection' button links to the settings page.